[Computational Systems Biology Group @CNB-CSIC]
JDet is a multiplatform software for the interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures. It contains the set of tools and features we consider critical for the daily work with this kind of data, and that previously were disseminated in different packages and web servers. The package includes two of our recently developed programs for extracting this kind of information from protein alignments. JDet can be extended via plugins to implement other methods or parse their results.
For a general description of the package and the biological problem which prompted its development, as well as more information on multiple sequence alignments (MSAs), conserved positions, specificity determining positions (SDPs), etc., please take a look at the following article: Muth et al. (2012). Bioinformatics 28 (4): 584-586.; and the references cited there, specially Pazos et al. (2006) Bioinformatics. 22(12):1440-1448 and Rausell et al. (2010) PNAS. 107(5)1995-2000
- Binaries: JDet_1.4.8.zip. The .zip file contains a multiplatform distribution of JDet that was tested in recent versions of Linux, MS-Windows and Mac OSX. Command-line versions of Xdet and S3Det are also included (see below). This file also contains instalation instructions, examples and documentation.
We have detected a bug in the S3Det version incorporated in the current JDet packages. While it is far from being critical, it could produce nonsense results in some very specific cases. While we incorporate in JDet the corrected files, you can download and compile the S3Det version included in the ChromDet package, corrected by David de Juan: https://github.com/david-juan/ChromDet.
- Source code: JDet is open source under Apache License 2.0, and the code can be downloaded from GitHub. You are welcome to contribute to the project.
- Plugins: JDet can be extended with plugins writen in Java. Methods for extracting important positions from alignments, or filters for parsing method results can be added to JDet with this system. A plugin for parsing Conseq/Consurf results is included with the distribution. We will maintain here a repository of plugins as more of these are developed. From a user point of view, installing plugins is just copying .jar files into JDet's directory. More information is given in the User Manual below. Here you can find detailed information for developers on how to code plugins for JDet, including example code, etc.
Here you can find on-line versions of the user manual and the guided tutorial. These are also included in the dowloadable distribution.
A list of known bugs is available, please read it. If you want to report new bugs or be noticed about new versions and fixed bugs please send an email to Juan A. Garcia Martin ().
Please cite the following reference when reporting any data or image generated with the program:
Thilo Muth, Juan A. Garcia-Martin, Antonio Rausell, David Juan, Alfonso Valencia & Florencio Pazos (2012).
JDet: Interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures. Bioinformatics 28(4): 584-586.
Included software and licenses
JDet includes binary distributions of two functional residue detection programs, Xdet and S3Det. These binaries can be also used outside the JDet environment, directly from the command line, e.g. for massive/batch runs (see Documentation above).
- Antonio del Sol, Florencio Pazos & Alfonso Valencia.
(2003). Automatic Methods for Predicting Functionally Important
Residues. Journal of Molecular Biology. 326(4):1289-1302.
- Florencio Pazos, Antonio Rausell & Alfonso Valencia. (2006).
Phylogeny-independent detection of functional residues.
Command line versions of Xdet are also distributed independently of JDet. Binaries of Xdet for different architectures are available upon request. Contact Florencio Pazos ().
Antonio Rausell, David Juan, Florencio Pazos & Alfonso Valencia. (2010).
Protein interactions and ligand binding: From protein subfamilies to functional specificity.
Proc Natl Acad Sci USA.
Command line versions of S3det are also distributed independently of JDet. Binaries
for different architectures as well as the source code are available upon request. Contact Antonio Rausell
JDet uses Java3DTM, for research and instructional Use
JDet also includes the Jmol plugin: Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/
Other third-party libraries are referenced in JDet's site at Google Code
For general questions/queries about the software, please contact Florencio Pazos (), for technical questions contact Juan A. Garcia Martin ().
[Computational Systems Biology Group @CNB-CSIC]